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Release 0.2.0

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@dfornika dfornika released this 03 Jan 23:16
· 1 commit to master since this release
0.2.0
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Learn about vigilant mode.

IRIDA Line-List Metadata

  • For each gene in the 'gene screening file', both the 'detection status' (True/False) and the detected allele
    are written to the IRIDA line-list. Alleles are also reported in the 'gene_detection_status.tsv' output file.

Parameters

  • Limited pipeline parameters to simplify and standardize operation
    • Resistance Gene Database is fixed on CARD database.
    • Cannot disable post-assembly correction or read trimming.
    • Cannot change contig name format
    • Cannot provide 'extra spades options' to shovill assembler
  • Added thresholds for resistance gene %Coverage and %Identity during secondary screening phase

Output

  • The gene screening file used for the analysis is included in the pipeline output
Assets 3
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